tbuckley/cabot-search huggingface dataset:
Neurodegenerative Disease Tauopathies
Authors: Benjamin C. Creekmore, Ryohei Watanabe, Edward B. Lee
Journal: Annual Review of Pathology Mechanisms of Disease (2023)

Tauopathies are a diverse group of progressive and fatal neurodegenerative diseases characterized by aberrant tau inclusions in the central nervous system. Tau protein forms pathologic fibrillar aggregates that are typically closely associated with neuronal cell death, leading to varied clinical phenotypes including dementia, movement disorders, and motor neuron disease. In this review, we describe the clinicopathologic features of tauopathies and highlight recent advances in understanding the mechanisms that lead to spread of pathologic aggregates through interconnected neuronal pathways. The cell-to-cell propagation of tauopathy is then linked to posttranslational modifications, tau fibril structural variants, and the breakdown of cellular protein quality control.
UPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics
Authors: JiaXuan Li, GuangCheng Han, Xiao Tian, Dan Liang, Peng Zhang
Journal: Molecular Biology and Evolution (2023)

Amplicon capture is a promising target sequence capture approach for phylogenomic analyses, and the design of clade-specific nuclear protein-coding locus (NPCL) amplification primers is crucial for its successful application. In this study, we developed a primer design program called UPrimer that can quickly design clade-specific NPCL amplification primers based on genome data, without requiring manual intervention. Unlike other available primer design programs, UPrimer uses a nested-PCR strategy that greatly improves the amplification success rate of the designed primers. We examined all available metazoan genome data deposited in NCBI and developed NPCL primer sets for 21 metazoan groups with UPrimer, covering a wide range of taxa, including arthropods, mollusks, cnidarians, echinoderms, and vertebrates. On average, each clade-specific NPCL primer set comprises ∼1,000 NPCLs. PCR amplification tests were performed in 6 metazoan groups, and the developed primers showed a PCR success rate exceeding 95%. Furthermore, we demonstrated a phylogenetic case study in Lepidoptera, showing how NPCL primers can be used for phylogenomic analyses with amplicon capture. Our results indicated that using 100 NPCL probes recovered robust high-level phylogenetic relationships among butterflies, highlighting the utility of the newly designed NPCL primer sets for phylogenetic studies. We anticipate that the automated tool UPrimer and the developed NPCL primer sets for 21 metazoan groups will enable researchers to obtain phylogenomic data more efficiently and cost-effectively and accelerate the resolution of various parts of the Tree of Life.
When I use a word . . . Medicines regulation: 1540 and all that
Authors: Jeffrey K Aronson
Journal: BMJ (2023)

The 1540 Pharmacy Wares, Drugs and Stuffs Act, also called the Apothecary Wares, Drugs and Stuffs Act, promulgated by Henry VIII, who had founded the College of Physicians in 1518, gave physicians the right to search apothecaries’ shops for faulty wares. If the search unearthed medicines that were defective in any way, they were to be destroyed. The act gave physicians power over apothecaries, who were also prohibited from supplying medicines unless under a physician’s prescription or a written note from the purchaser. It also provided income for the King9s purse, since there was a fine for failing to comply with the act. It would be some time before quality, efficacy, and safety became the main concerns of medicines regulators.
Use of Artificial Intelligence Techniques to Assist Individuals with Physical Disabilities
Authors: Sidharth Pancholi, Juan P. Wachs, Bradley S. Duerstock
Journal: Annual Review of Biomedical Engineering (2023)

Assistive technologies (AT) enable people with disabilities to perform activities of daily living more independently, have greater access to community and healthcare services, and be more productive performing educational and/or employment tasks. Integrating artificial intelligence (AI) with various agents, including electronics, robotics, and software, has revolutionized AT, resulting in groundbreaking technologies such as mind-controlled exoskeletons, bionic limbs, intelligent wheelchairs, and smart home assistants. This article provides a review of various AI techniques that have helped those with physical disabilities, including brain–computer interfaces, computer vision, natural language processing, and human–computer interaction. The current challenges and future directions for AI-powered advanced technologies are also addressed.
Deep learning system improved detection efficacy of fetal intracranial malformations in a randomized controlled trial
Authors: Meifang Lin, Qian Zhou, Ting Lei, Ning Shang, Qiao zheng, Xiaoqin He, Nan Wang, Hongning Xie
Journal: npj Digital Medicine (2023)

Abstract Congenital malformations of the central nervous system are among the most common major congenital malformations. Deep learning systems have come to the fore in prenatal diagnosis of congenital malformation, but the impact of deep learning-assisted detection of congenital intracranial malformations from fetal neurosonographic images has not been evaluated. Here we report a three-way crossover, randomized control trial (Trial Registration: ChiCTR2100048233) that assesses the efficacy of a deep learning system, the Prenatal Ultrasound Diagnosis Artificial Intelligence Conduct System (PAICS), in assisting fetal intracranial malformation detection. A total of 709 fetal neurosonographic images/videos are read interactively by 36 sonologists of different expertise levels in three reading modes: unassisted mode (without PAICS assistance), concurrent mode (using PAICS at the beginning of the assessment) and second mode (using PAICS after a fully unaided interpretation). Aided by PAICS, the average accuracy of the unassisted mode (73%) is increased by the concurrent mode (80%; P &lt; 0.001) and the second mode (82%; P &lt; 0.001). Correspondingly, the AUC is increased from 0.85 to 0.89 and to 0.90, respectively ( P &lt; 0.001 for all). The median read time per data is slightly increased in concurrent mode but substantially prolonged in the second mode, from 6 s to 7 s and to 11 s ( P &lt; 0.001 for all). In conclusion, PAICS in both concurrent and second modes has the potential to improve sonologists’ performance in detecting fetal intracranial malformations from neurosonographic data. PAICS is more efficient when used concurrently for all readers.
Prognostic indices in diffuse large B-cell lymphoma: a population-based comparison and validation study of multiple models
Authors: Jelena Jelicic, Karen Juul-Jensen, Zoran Bukumiric, Michael Roost Clausen, Ahmed Ludvigsen Al-Mashhadi, Robert Schou Pedersen, Christian Bjørn Poulsen, Peter Brown, Tarec Christoffer El-Galaly, Thomas Stauffer Larsen
Journal: Blood Cancer Journal (2023)

Currently, the International Prognostic Index (IPI) is the most used and reported model for prognostication in patients with newly diagnosed diffuse large B-cell lymphoma (DLBCL). IPI-like variations have been proposed, but only a few have been validated in different populations (e.g., revised IPI (R-IPI), National Comprehensive Cancer Network IPI (NCCN-IPI)). We aimed to validate and compare different IPI-like variations to identify the model with the highest predictive accuracy for survival in newly diagnosed DLBCL patients. We included 5126 DLBCL patients treated with immunochemotherapy with available data required by 13 different prognostic models. All models could predict survival, but NCCN-IPI consistently provided high levels of accuracy. Moreover, we found similar 5-year overall survivals in the high-risk group (33.4%) compared to the original validation study of NCCN-IPI. Additionally, only one model incorporating albumin performed similarly well but did not outperform NCCN-IPI regarding discrimination (c-index 0.693). Poor fit, discrimination, and calibration were observed in models with only three risk groups and without age as a risk factor. In this extensive retrospective registry-based study comparing 13 prognostic models, we suggest that NCCN-IPI should be reported as the reference model along with IPI in newly diagnosed DLBCL patients until more accurate validated prognostic models for DLBCL become available.
Selected Articles from This Issue
Journal: Clinical Cancer Research (2023)

Highlights| October 13 2023 Selected Articles from This Issue Author & Article Information Online ISSN: 1557-3265 Print ISSN: 1078-0432 ©2023 American Association for Cancer Research2023American Association for Cancer Research Clin Cancer Res (2023) 29 (20): 4019. https://doi.org/10.1158/1078-0432.CCR-29-20-HI Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Article Versions Icon Versions Version of Record October 13 2023 Citation Selected Articles from This Issue. Clin Cancer Res 15 October 2023; 29 (20): 4019. https://doi.org/10.1158/1078-0432.CCR-29-20-HI Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest Search Advanced Search Treatment options for hepatocellular carcinoma (HCC) patients presenting with portal vein tumor thrombus (PVTT) are limited, but recent clinical studies have shown promising results using combination therapies, including the anti-PD-1 immunotherapeutic camrelizumab and the VEGFR2 inhibitor apatinib. Additionally, advances in stereotactic body radiotherapy (SBRT) facilitate targeting high doses of radiation to tumors while reducing damage to neighboring healthy tissue. In a prospective study, Hu and colleagues assess the safety and efficacy of camrelizumab plus apatinib treatment with or without SBRT as first-line therapy for HCC patients with PVTT. The authors found that safety profiles were similar among patients who received SBRT and those who did not, with 21.7% of patients reporting grade ≥3 treatment-related adverse events. The SBRT-treated cohort had a median overall survival (OS) of 12.7 months and a median progression-free survival (PFS) of 4.6 months compared with the non-SBRT-treated cohort (median OS 8.6 months; median PFS 2.5 months).... You do not currently have access to this content.
Covid-19: Confusion around vaccination during pregnancy likely to have contributed to deaths of 27 women in the UK
Authors: Matthew Limb
Journal: BMJ (2023)

Covid-19: Confusion around vaccination during pregnancy likely to have contributed to deaths of 27 women in the UK Matthew LimbPregnant women are being urged to get the covid vaccine after an expert group found that "confused messaging and vaccine hesitancy" may have contributed to the deaths of 27 women during the pandemic in the UK. 1
The influence of immunodeficiency, disease features, and patient characteristics on survival in plasmablastic lymphoma
Authors: Pietro R. Di Ciaccio, Mark N. Polizzotto, Kate Cwynarski, Alina S. Gerrie, Catherine Burton, Mark Bower, John Kuruvilla, Silvia Montoto, Pam McKay, Christopher P. Fox, Samuel Milliken, Awachana Jiamsakul, Wendy Osborne, Graham P. Collins, Kate Manos, Kim M. Linton, Sunil Iyengar, Shireen Kassam, Michelle Poon Limei, David Kliman, Nicole Wong Doo, Anne-Marie Watson, Pasquale Fedele, Costas K. Yannakou, Stewart Hunt, Matthew Ku, Laurie H. Sehn, Alexandra Smith, Hanna Renshaw, Alice Maxwell, Qin Liu, Rageshri Dhairyawan, Graeme Ferguson, Keir Pickard, Daniel Painter, Nisha Thakrar, Kevin W. Song, Nada Hamad
Journal: Blood (2023)
<i>Plasmodium falciparum</i> exploits CD44 as a coreceptor for erythrocyte invasion
Authors: Barbara Baro, Chi Yong Kim, Carrie Lin, Angel K. Kongsomboonvech, Marilou Tetard, Nana Ansuah Peterson, Nichole D. Salinas, Niraj H. Tolia, Elizabeth S. Egan
Journal: Blood (2023)

The malaria parasite Plasmodium falciparum invades and replicates asexually within human erythrocytes. CD44 expressed on erythrocytes was previously identified as an important host factor for P falciparum infection through a forward genetic screen, but little is known about its regulation or function in these cells, nor how it may be used by the parasite. We found that CD44 can be efficiently deleted from primary human hematopoietic stem cells using CRISPR/Cas9 genome editing, and that the efficiency of ex vivo erythropoiesis to enucleated cultured red blood cells (cRBCs) is not affected by lack of CD44. However, the rate of P falciparum invasion was reduced in CD44-null cRBCs relative to isogenic wild-type control cells, validating CD44 as an important host factor for this parasite. We identified 2 P falciparum invasion ligands as binding partners for CD44, erythrocyte binding antigen 175 (EBA-175) and EBA-140 and demonstrated that their ability to bind to human erythrocytes relies primarily on their canonical receptors, glycophorin A and glycophorin C, respectively. We further show that EBA-175 induces phosphorylation of erythrocyte cytoskeletal proteins in a CD44-dependent manner. Our findings support a model in which P falciparum exploits CD44 as a coreceptor during invasion of human erythrocytes, stimulating CD44-dependent phosphorylation of host cytoskeletal proteins that alter host cell deformability and facilitate parasite entry.
Mice expressing nonpolymerizable fibrinogen have reduced arterial and venous thrombosis with preserved hemostasis
Authors: Woosuk S. Hur, Tomohiro Kawano, Jean Marie N. Mwiza, David S. Paul, Robert H. Lee, Emily G. Clark, Emma G. Bouck, Ananya Dutta, Can Cai, Stephen R. Baker, Martin Guthold, Nigel Mackman, Pierre Mangin, Alisa S. Wolberg, Wolfgang Bergmeier, Matthew J. Flick
Journal: Blood (2023)
Mutated IKZF1 is an independent marker of adverse risk in acute myeloid leukemia
Authors: Jan-Niklas Eckardt, Sebastian Stasik, Christoph Röllig, Andreas Petzold, Tim Sauer, Sebastian Scholl, Andreas Hochhaus, Martina Crysandt, Tim H. Brümmendorf, Ralph Naumann, Björn Steffen, Volker Kunzmann, Hermann Einsele, Markus Schaich, Andreas Burchert, Andreas Neubauer, Kerstin Schäfer-Eckart, Christoph Schliemann, Stefan W. Krause, Regina Herbst, Mathias Hänel, Maher Hanoun, Ulrich Kaiser, Martin Kaufmann, Zdenek Rácil, Jiri Mayer, Uta Oelschlägel, Wolfgang E. Berdel, Gerhard Ehninger, Hubert Serve, Carsten Müller-Tidow, Uwe Platzbecker, Claudia D. Baldus, Andreas Dahl, Johannes Schetelig, Martin Bornhäuser, Jan Moritz Middeke, Christian Thiede
Journal: Leukemia (2023)

Abstract Genetic lesions of IKZF1 are frequent events and well-established markers of adverse risk in acute lymphoblastic leukemia. However, their function in the pathophysiology and impact on patient outcome in acute myeloid leukemia (AML) remains elusive. In a multicenter cohort of 1606 newly diagnosed and intensively treated adult AML patients, we found IKZF1 alterations in 45 cases with a mutational hotspot at N159S. AML with mutated IKZF1 was associated with alterations in RUNX1 , GATA2 , KRAS , KIT , SF3B1 , and ETV6 , while alterations of NPM1 , TET2 , FLT3 -ITD, and normal karyotypes were less frequent. The clinical phenotype of IKZF1 -mutated AML was dominated by anemia and thrombocytopenia. In both univariable and multivariable analyses adjusting for age, de novo and secondary AML, and ELN2022 risk categories, we found mutated IKZF1 to be an independent marker of adverse risk regarding complete remission rate, event-free, relapse-free, and overall survival. The deleterious effects of mutated IKZF1 also prevailed in patients who underwent allogeneic hematopoietic stem cell transplantation ( n = 519) in both univariable and multivariable models. These dismal outcomes are only partially explained by the hotspot mutation N159S. Our findings suggest a role for IKZF1 mutation status in AML risk modeling.
Narcissistic dimensions and depressive symptoms in patients across mental disorders in cognitive behavioural therapy and in psychoanalytic interactional therapy in Germany: a prospective cohort study
Authors: Maike Richter, Simon Mota, Leonie Hater, Rebecca Bratek, Janik Goltermann, Carlotta Barkhau, Marius Gruber, Jonathan Repple, Michael Storck, Rogério Blitz, Dominik Grotegerd, Oliver Masuhr, Ulrich Jaeger, Bernhard T Baune, Martin Dugas, Martin Walter, Udo Dannlowski, Ulrike Buhlmann, Mitja Back, Nils Opel
Journal: The Lancet Psychiatry (2023)
Pembrolizumab plus lenvatinib in second-line and third-line patients with pleural mesothelioma (PEMMELA): a single-arm phase 2 study
Authors: Li-Anne H Douma, Ferry Lalezari, Vincent van der Noort, Jeltje F de Vries, Kim Monkhorst, Illaa Smesseim, Paul Baas, Bodien Schilder, Marrit Vermeulen, Jacobus A Burgers, Cornedine J de Gooijer
Journal: The Lancet Oncology (2023)
Accuracy of package inserts of SARS-CoV-2 rapid antigen tests: a secondary analysis of manufacturer versus systematic review data
Authors: Jacob Bigio, Emily L-H MacLean, Rishav Das, Giorgia Sulis, Mikashmi Kohli, Sarah Berhane, Jacqueline Dinnes, Jonathan J Deeks, Lukas E Brümmer, Claudia M Denkinger, Madhukar Pai
Journal: The Lancet Microbe (2023)
Tailored immunotherapy approach with nivolumab with or without nivolumab plus ipilimumab as immunotherapeutic boost in patients with metastatic renal cell carcinoma (TITAN-RCC): a multicentre, single-arm, phase 2 trial
Authors: Marc-Oliver Grimm, Emilio Esteban, Philippe Barthélémy, Manuela Schmidinger, Jonas Busch, Begoña P Valderrama, Natalie Charnley, Marc Schmitz, Ulrike Schumacher, Katharina Leucht, Susan Foller, Gustavo Baretton, Ignacio Duran, Guillermo de Velasco, Frank Priou, Pablo Maroto, Laurence Albiges, Carlo Barone, Daniel Castellano, Christine Chevreau, Pablo Gajate Borau, Srinavasan Gopalakrishnan, Enrique Grande, Abdel Hamid, Julia Heinzelbecker, Martin Janssen, Jindřich Kopecký, Eugen Kubala, Wolfgang Loidl, Anja Lorch, Bohuslav Melichar, Nuria Lainez Milagro, Günter Niegisch, Carsten Ohlmann, Anne Sacré, Naveed Sarwar, Giovanni Schinzari, Dirk Schrijvers, Sophie Tartas, Manfred Wirth, Pascal Wolter, Milanda Zemanova
Journal: The Lancet Oncology (2023)
Nanotechnology-based techniques for hair follicle regeneration
Authors: Mafalda Correia, Joana Lopes, Daniela Lopes, Ana Melero, Pooyan Makvandi, Francisco Veiga, Jorge F.J. Coelho, Ana C. Fonseca, Ana Cláudia Paiva-Santos
Journal: Biomaterials (2023)

The hair follicle (HF) is a multicellular complex structure of the skin that contains a reservoir of multipotent stem cells. Traditional hair repair methods such as drug therapies, hair transplantation, and stem cell therapy have limitations. Advances in nanotechnology offer new approaches for HF regeneration, including controlled drug release and HF-specific targeting. Until recently, embryogenesis was thought to be the only mechanism for forming hair follicles. However, in recent years, the phenomenon of wound-induced hair neogenesis (WIHN) or de novo HF regeneration has gained attention as it can occur under certain conditions in wound beds. This review covers HF-specific targeting strategies, with particular emphasis on currently used nanotechnology-based strategies for both hair loss-related diseases and HF regeneration. HF regeneration is discussed in several modalities: modulation of the hair cycle, stimulation of progenitor cells and signaling pathways, tissue engineering, WIHN, and gene therapy. The HF has been identified as an ideal target for nanotechnology-based strategies for hair regeneration. However, some regulatory challenges may delay the development of HF regeneration nanotechnology based-strategies, which will be lastly discussed.
Impact of COVID-19 on immunocompromised populations during the Omicron era: insights from the observational population-based INFORM study
Authors: Rachael A. Evans, Sabada Dube, Yi Lu, Mark Yates, Sofie Arnetorp, Eleanor Barnes, Samira Bell, Lucy Carty, Kathryn Evans, Sophie Graham, Nahila Justo, Paul Moss, Sudhir Venkatesan, Renata Yokota, Catia Ferreira, Richard McNulty, Sylvia Taylor, Jennifer K. Quint
Journal: The Lancet Regional Health - Europe (2023)

Immunocompromised individuals are not optimally protected by COVID-19 vaccines and potentially require additional preventive interventions to mitigate the risk of severe COVID-19. We aimed to characterise and describe the risk of severe COVID-19 across immunocompromised groups as the pandemic began to transition to an endemic phase.
Pre-existing inflammatory disease predicts cutaneous immunotherapy toxicity development: A multi-institutional cohort study
Authors: Guihong Wan, Nga Nguyen, Bonnie W. Leung, Hannah Rashdan, Kimberly Tang, Katie Roster, Michael R. Collier, Pearl O. Ugwu-Dike, Neel S. Raval, Nora A. Alexander, Ruple Jairath, Jordan Phillipps, Munachimso Amadife, Shijia Zhang, Alexander Gusev, Steven T. Chen, Kerry L. Reynolds, Nicole R. LeBoeuf, Shawn G. Kwatra, Yevgeniy R. Semenov
Journal: Journal of the American Academy of Dermatology (2023)
Who has skin in the game? Expanding patient opportunities for research engagement is a win–win for dermatology
Authors: Annelise Colvin, Lynn Petukhova
Journal: British Journal of Dermatology (2023)

Journal Article Corrected proof Who has skin in the game? Expanding patient opportunities for research engagement is a win–win for dermatology Get access Annelise Colvin, Annelise Colvin Writing - original draft, Writing - review & editing Vagelos College of Physicians and Surgeons https://orcid.org/0000-0003-1703-6854 Search for other works by this author on: Oxford Academic Google Scholar Lynn Petukhova Lynn Petukhova Conceptualization, Project administration, Writing - review & editing Department of Epidemiology, Mailman School of Public HealthDepartment of Dermatology, College of Physicians & Surgeons, Columbia University, New York, NY, USA Correspondence: Lynn Petukhova. Email: lynn.petukhova@columbia.edu https://orcid.org/0000-0002-1573-1653 Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, ljad394, https://doi.org/10.1093/bjd/ljad394 Published: 13 October 2023 Article history Received: 01 October 2023 Accepted: 06 October 2023 Published: 13 October 2023 Corrected and typeset: 02 November 2023
Identification of potential common genetic modifiers of neurofibromas: a genome-wide association study in 1333 patients with neurofibromatosis type 1
Authors: Laurence Pacot, Audrey Sabbagh, Pierre Sohier, Djihad Hadjadj, Manuela Ye, Anne Boland-Auge, Delphine Bacq-Daian, Ingrid Laurendeau, Audrey Briand-Suleau, Jean-François Deleuze, Raphaël Margueron, Michel Vidaud, Salah Ferkal, Béatrice Parfait, Dominique Vidaud, Henri Adamski, Clarisse Baumann-Morel, Christine Bellanné, Eric Biet, Pascal Bousque, Christian Brand, Xavier Balguerie, Pierre Castelnau, Yves Chaix, Jacqueline Chevrant-Breton, Evelyne Collet, Jean-François Cuny, Pascal Chastagner, Marie-Lorraine Chandeclerc, Emmanuel Cheuret, Pascal Cintas, Helene Dollfus, Christian Derancourt, Valérie Drouin-Garraud, Michel d’Incan, Hélène De Leersnyder, Olivier Dereure, Diane Doumar, Nicolas Fabre, Vincenza Ferraro, Christine Francannet, Laurence Faivre, Florence Fellmann, Nathalie Feugier Dominique Gaillard, Alice Goldenberg, Lucie Guyant-Marechal, Bernard Guillot, Jean-Sebastien Guillamo, Smaïl Hadj-Rabia, Dominique Hamel-Teillac, Isabelle Kemlin, Jean-Philippe Lacour, Veronique Laithier, Nathalie Lesavre, Stanislas Lyonnet, Kim Maincent, Sophie Maradeix, Laurent Machet, Eva Mansat, Nicolas Meyer, Monique Mozelle, Jean Christophe Moreno Celine Moret, Eric Puzenat, Stéphane Pinson, Diana Rodriguez, Jean-François Stalder, Elisabeth Schweitzer, Claire Thalamas, Christel Thauvin, Alain Verloes, Jacques Zeller, Eric Pasmant, Pierre Wolkenstein
Journal: British Journal of Dermatology (2023)

Neurofibromatosis type 1 (NF1) is characterized by the highly variable and unpredictable development of benign peripheral nerve sheath tumours: cutaneous (cNFs), subcutaneous (scNFs) and plexiform (pNFs) neurofibromas.